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- PDB-9r3h: Structure of liver pyruvate kinase in complex with fluorescent pr... -

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Basic information

Entry
Database: PDB / ID: 9r3h
TitleStructure of liver pyruvate kinase in complex with fluorescent probe 4b
ComponentsIsoform L-type of Pyruvate kinase PKLR
KeywordsTRANSFERASE / Pyruvate kinase / fluorescence / allosteric site
Function / homology
Function and homology information


pyruvate kinase complex / pyruvate biosynthetic process / SARS-CoV-1-host interactions / ChREBP activates metabolic gene expression / pyruvate kinase / pyruvate kinase activity / Pyruvate metabolism / monosaccharide binding / response to metal ion / Glycolysis ...pyruvate kinase complex / pyruvate biosynthetic process / SARS-CoV-1-host interactions / ChREBP activates metabolic gene expression / pyruvate kinase / pyruvate kinase activity / Pyruvate metabolism / monosaccharide binding / response to metal ion / Glycolysis / response to ATP / potassium ion binding / Regulation of gene expression in beta cells / response to cAMP / response to glucose / cellular response to epinephrine stimulus / response to nutrient / glycolytic process / cellular response to insulin stimulus / kinase activity / response to hypoxia / magnesium ion binding / extracellular exosome / ATP binding / cytosol / cytoplasm
Similarity search - Function
Pyruvate kinase, active site / Pyruvate kinase active site signature. / Pyruvate kinase / Pyruvate kinase, barrel / Pyruvate kinase, insert domain superfamily / Pyruvate kinase, barrel domain / Pyruvate kinase, C-terminal / Pyruvate kinase, C-terminal domain superfamily / Pyruvate kinase, alpha/beta domain / Pyruvate kinase-like, insert domain superfamily ...Pyruvate kinase, active site / Pyruvate kinase active site signature. / Pyruvate kinase / Pyruvate kinase, barrel / Pyruvate kinase, insert domain superfamily / Pyruvate kinase, barrel domain / Pyruvate kinase, C-terminal / Pyruvate kinase, C-terminal domain superfamily / Pyruvate kinase, alpha/beta domain / Pyruvate kinase-like, insert domain superfamily / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily
Similarity search - Domain/homology
: / 1,6-di-O-phosphono-beta-D-fructofuranose / : / OXALATE ION / Pyruvate kinase PKLR
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBogucka, A. / Nilsson, O. / Grotli, M. / Hyvonen, M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust223804/Z/21/Z United Kingdom
CitationJournal: Eur.J.Med.Chem. / Year: 2025
Title: Fluorescent binding assay for allosteric ligands of liver pyruvate kinase.
Authors: Nilsson, O. / Bogucka, A. / Koteles, I. / Haversen, L. / Liljenberg, S. / Rutberg, M. / Hyvonen, M. / Grotli, M.
History
DepositionMay 5, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 13, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Isoform L-type of Pyruvate kinase PKLR
B: Isoform L-type of Pyruvate kinase PKLR
C: Isoform L-type of Pyruvate kinase PKLR
D: Isoform L-type of Pyruvate kinase PKLR
E: Isoform L-type of Pyruvate kinase PKLR
F: Isoform L-type of Pyruvate kinase PKLR
G: Isoform L-type of Pyruvate kinase PKLR
H: Isoform L-type of Pyruvate kinase PKLR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)392,03744
Polymers386,2838
Non-polymers5,75436
Water40,5522251
1
A: Isoform L-type of Pyruvate kinase PKLR
B: Isoform L-type of Pyruvate kinase PKLR
C: Isoform L-type of Pyruvate kinase PKLR
D: Isoform L-type of Pyruvate kinase PKLR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,01922
Polymers193,1424
Non-polymers2,87718
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22510 Å2
ΔGint-131 kcal/mol
Surface area56660 Å2
MethodPISA
2
E: Isoform L-type of Pyruvate kinase PKLR
F: Isoform L-type of Pyruvate kinase PKLR
G: Isoform L-type of Pyruvate kinase PKLR
H: Isoform L-type of Pyruvate kinase PKLR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,01922
Polymers193,1424
Non-polymers2,87718
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22280 Å2
ΔGint-131 kcal/mol
Surface area56340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)208.521, 112.553, 189.315
Angle α, β, γ (deg.)90, 91.09, 90
Int Tables number5
Space group name H-MC121

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Components

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Protein / Sugars , 2 types, 16 molecules ABCDEFGH

#1: Protein
Isoform L-type of Pyruvate kinase PKLR / Pyruvate kinase 1 / Pyruvate kinase isozymes L/R / R-type/L-type pyruvate kinase / Red cell/liver ...Pyruvate kinase 1 / Pyruvate kinase isozymes L/R / R-type/L-type pyruvate kinase / Red cell/liver pyruvate kinase


Mass: 48285.379 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PKLR, PK1, PKL / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P30613, pyruvate kinase
#2: Sugar
ChemComp-FBP / 1,6-di-O-phosphono-beta-D-fructofuranose / BETA-FRUCTOSE-1,6-DIPHOSPHATE / FRUCTOSE-1,6-BISPHOSPHATE / 1,6-di-O-phosphono-beta-D-fructose / 1,6-di-O-phosphono-D-fructose / 1,6-di-O-phosphono-fructose


Type: D-saccharide, beta linking / Mass: 340.116 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C6H14O12P2
IdentifierTypeProgram
b-D-Fruf1PO36PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 5 types, 2279 molecules

#3: Chemical
ChemComp-OXL / OXALATE ION


Mass: 88.019 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2O4
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: K
#6: Chemical
ChemComp-A1JB3 / 4-[4-[(7-azanyl-2,1,3-benzoxadiazol-4-yl)sulfonyl]piperazin-1-yl]sulfonylbenzene-1,2-diol / BEHXKSOMSFVUBW-UHFFFAOYSA-N


Mass: 455.465 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H17N5O7S2 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2251 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.88 Å3/Da / Density % sol: 57.22 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM HEPES/MOPS, 10% PEG8000, 20% ethylene glycol, 10 mM phenylalanine, 20 mM sodium oxalate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.95374 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Mar 14, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95374 Å / Relative weight: 1
ReflectionResolution: 2.1→189.281 Å / Num. obs: 207434 / % possible obs: 93.8 % / Redundancy: 7.2 %
Details: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last ...Details: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last updated 2020-04-13: http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Index/) and the actual quantities provided by MRFANA (https://github.com/githubgphl/MRFANA) from the autoPROC package (https://www.globalphasing.com/autoproc/). In general, the mmCIF categories here should provide items that are currently used in the PDB archive. If there are alternatives, the one recommended by the PDB developers has been selected. The distinction between *_all and *_obs quantities is not always clear: often only one version is actively used within the PDB archive (or is the one recommended by PDB developers). The intention of distinguishing between classes of reflections before and after some kind of observation criterion was applied, can in principle be useful - but such criteria change in various ways throughout the data processing steps (rejection of overloaded or too partial reflections, outlier/misfit rejections during scaling etc) and there is no retrospect computation of data scaling/merging statistics for the reflections used in the final refinement (where another observation criterion might have been applied). Typical data processing will usually only provide one version of statistics at various stages and these are given in the recommended item here, irrespective of the "_all" and "_obs" connotation, see e.g. the use of _reflns.pdbx_Rmerge_I_obs, _reflns.pdbx_Rrim_I_all and _reflns.pdbx_Rpim_I_all. Please note that all statistics related to "merged intensities" (or "merging") are based on inverse-variance weighting of the individual measurements making up a symmetry-unique reflection. This is standard for several decades now, even if some of the dictionary definitions seem to suggest that a simple "mean" or "average" intensity is being used instead. R-values are always given for all symmetry-equivalent reflections following Friedel's law, i.e. Bijvoet pairs are not treated separately (since we want to describe the overall mean intensity and not the mean I(+) and I(-) here). The Rrim metric is identical to the Rmeas R-value and only differs in name. _reflns.pdbx_number_measured_all is the number of measured intensities just before the final merging step (at which point no additional rejection takes place). _reflns.number_obs is the number of symmetry-unique observations, i.e. the result of merging those measurements via inverse-variance weighting. _reflns.pdbx_netI_over_sigmaI is based on the merged intensities (_reflns.number_obs) as expected. _reflns.pdbx_redundancy is synonymous with "multiplicity". The per-shell item _reflns_shell.number_measured_all corresponds to the overall value _reflns.pdbx_number_measured_all. The per-shell item _reflns_shell.number_unique_all corresponds to the overall value _reflns.number_obs. The per-shell item _reflns_shell.percent_possible_all corresponds to the overall value _reflns.percent_possible_obs. The per-shell item _reflns_shell.meanI_over_sigI_obs corresponds to the overall value given as _reflns.pdbx_netI_over_sigmaI. But be aware of the incorrect definition of the former in the current dictionary!
CC1/2: 0.995 / CC1/2 anomalous: -0.225 / Rmerge(I) obs: 0.1607 / Rpim(I) all: 0.0642 / Rrim(I) all: 0.1732 / AbsDiff over sigma anomalous: 0.766 / Baniso tensor eigenvalue 1: 0 Å2 / Baniso tensor eigenvalue 2: 14.3156 Å2 / Baniso tensor eigenvalue 3: 20.8424 Å2 / Baniso tensor eigenvector 1 ortho1: 0.8698 / Baniso tensor eigenvector 1 ortho2: 0 / Baniso tensor eigenvector 1 ortho3: -0.4933 / Baniso tensor eigenvector 2 ortho1: 0 / Baniso tensor eigenvector 2 ortho2: 1 / Baniso tensor eigenvector 2 ortho3: 0 / Baniso tensor eigenvector 3 ortho1: 0.4933 / Baniso tensor eigenvector 3 ortho2: 0 / Baniso tensor eigenvector 3 ortho3: 0.8698 / Aniso diffraction limit 1: 2.1 Å / Aniso diffraction limit 2: 2.176 Å / Aniso diffraction limit 3: 2.363 Å / Aniso diffraction limit axis 1 ortho1: 0.9661 / Aniso diffraction limit axis 1 ortho2: 0 / Aniso diffraction limit axis 1 ortho3: -0.25797 / Aniso diffraction limit axis 2 ortho1: 0 / Aniso diffraction limit axis 2 ortho2: 1 / Aniso diffraction limit axis 2 ortho3: 0 / Aniso diffraction limit axis 3 ortho1: 0.25797 / Aniso diffraction limit axis 3 ortho2: 0 / Aniso diffraction limit axis 3 ortho3: 0.9661 / Net I/σ(I): 7.4 / Num. measured all: 1493667 / Observed signal threshold: 1.2 / Orthogonalization convention: pdb / % possible anomalous: 93.7 / % possible ellipsoidal: 93.8 / % possible ellipsoidal anomalous: 93.7 / % possible spherical: 81.4 / % possible spherical anomalous: 81.3 / Redundancy anomalous: 3.65 / Signal type: local
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. measured obsNum. unique allNum. unique obsCC1/2CC1/2 anomalousRpim(I) allRrim(I) allAbsDiff over sigma anomalous% possible anomalous% possible ellipsoidal% possible ellipsoidal anomalous% possible spherical% possible spherical anomalousRedundancy anomalous% possible all
6.158-189.2817.20.048819.14746347463410372103720.998-0.4850.01950.05260.62799.710099.710099.73.75100
4.874-6.1576.650.077515.95689416894110371103710.995-0.2150.03250.08410.74799.910099.910099.93.41100
4.252-4.8747.190.074117.9745287452810372103720.994-0.3980.02970.07990.7191001001001001003.67100
3.86-4.2527.370.090416.07764237642310372103720.992-0.3280.03570.09720.7421001001001001003.75100
3.581-3.867.460.10914.01773847738410372103720.991-0.260.04280.11720.7641001001001001003.79100
3.368-3.5817.50.137311.68778237782310371103710.988-0.2560.05360.14750.7871001001001001003.81100
3.198-3.3687.460.17939.39773557735510372103720.984-0.1360.07030.19270.7911001001001001003.78100
3.058-3.1986.790.22737.28704127041210372103720.975-0.0680.09430.24640.80499.810099.810099.83.44100
2.94-3.0586.840.27776.13709767097610371103710.969-0.0720.11450.30080.79899.910099.910099.93.47100
2.838-2.946.520.35564.94676106761010372103720.952-0.0390.15120.3870.7961001001001001003.3100
2.748-2.8386.920.43164.32717687176810372103720.944-0.030.17680.46690.7931001001001001003.5100
2.67-2.7487.060.52323.72732167321610371103710.919-0.0230.21150.56480.781001001001001003.57100
2.599-2.677.140.63423.16740887408810372103720.89-0.0290.25450.68380.77899.799.799.799.799.73.6199.7
2.534-2.5997.220.73092.84749217492110372103720.865-0.0050.29150.78730.78398.798.798.798.798.73.6598.7
2.474-2.5347.30.85732.47757457574510372103720.848-0.0060.33970.92270.77595.995.795.995.795.93.6995.7
2.415-2.4747.371.01652.17764867648610371103710.791-0.0160.40071.09320.76690.890.490.890.490.83.7290.4
2.36-2.4157.441.11832.01771707717010372103720.773-0.0240.43871.20180.76486.686.386.686.386.63.7586.3
2.306-2.367.51.27751.84778247782410372103720.701-0.0050.49931.37210.76386.486.286.479.6803.7886.2
2.247-2.3067.611.53191.59788907889010371103710.641-0.0320.59471.64380.75584.784.784.767.868.23.8384.7
2.1-2.2477.471.75691.45774737747310372103720.534-0.0150.69181.88910.76955.355.455.322.222.23.7655.4

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Processing

Software
NameVersionClassificationNB
autoPROC1.0.5 20221121data processing
XDSJan 10, 2022data reduction
Aimless0.7.9data scaling
STARANISO2.3.90data scaling
BUSTER2.10.4refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→189.28 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.928 / SU R Cruickshank DPI: 0.257 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.266 / SU Rfree Blow DPI: 0.196 / SU Rfree Cruickshank DPI: 0.195
RfactorNum. reflection% reflectionSelection details
Rfree0.2333 10119 -RANDOM
Rwork0.2046 ---
obs0.206 207434 81.4 %-
Displacement parametersBiso mean: 39.35 Å2
Baniso -1Baniso -2Baniso -3
1-0.5527 Å20 Å2-0.5939 Å2
2---0.4835 Å20 Å2
3----0.0692 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: LAST / Resolution: 2.1→189.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25902 0 344 2251 28497
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00827169HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.936984HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d9663SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes4882HARMONIC5
X-RAY DIFFRACTIONt_it27050HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion3613SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact24440SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.98
X-RAY DIFFRACTIONt_other_torsion16.3
LS refinement shellResolution: 2.1→2.2 Å
RfactorNum. reflection% reflection
Rfree0.313 202 -
Rwork0.2745 --
obs0.2763 4149 12.46 %

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